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Difference between revisions of "Glycoside Hydrolase Family 55"

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* [[Author]]s: [[User:TakuyaIshida|Takuya Ishida]] and ^^^Kiyohiko Igarashi^^^
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* [[Author]]s: [[User:Takuya Ishida|Takuya Ishida]] and [[User:Kiyohiko Igarashi|Kiyohiko Igarashi]]
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* [[Responsible Curator]]:  [[User:Shinya Fushinobu|Shinya Fushinobu]]
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== Substrate specificities ==
 
== Substrate specificities ==
[[Glycoside Hydrolases]] of family 55 exclusively consists of &beta;-1,3-glucanases, including both exo- and endo-enzymes, at this moment. All of biochemically characterized members of this family have fungal origin, but not from yeast. Several homologous genes are found from Bacterial genomes, but none of their gene products are characterized.
+
[[Glycoside Hydrolases|Glycoside Hydrolase]] family 55 consists exclusively of &beta;-1,3-glucanases, including both [[exo]]- and [[endo]]-enzymes. All biochemically characterized members of this family had been limited to fungal enzymes until the extensive work by Bianchetti, Takasuka, et al., who reported the crystallography of [[exo]]-&beta;-1,3-glucanase SacteLam55A from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=862751 ''Streptmyces'' sp. SirexAA-E] ([http://www.uniprot.org/uniprot/G2NFJ9 Uniprot G2NFJ9]), together with characterization of many other bacterial enzymes <CITE>Bianchetti2015</CITE>.
 
 
The enzymes belonging to this family are generally called "laminarinase" because the enzyme hydrolyzes laminarin (&beta;-1,3-glucan having single &beta;-1,6-glucoside side chains: &beta;-1,3/1,6-glucan) from brown algae. But the physiological substrate for the enzymes might be fungal cell wall, whose major component is also &beta;-1,3/1,6-glucan.
 
  
The majority of the members in this family are exo-glucan-1,3-&beta;-glucosidases (EC[http://us.expasy.org/cgi-bin/nicezyme.pl?3.2.1.58 3.2.1.58]). Exo-&beta;-1,3-glucanases in this family cleave the terminal &beta;-1,3-glycosidic linkage at non-reducing end of &beta;-1,3-glucans or &beta;-1,3/1,6-glucans. Many of them produces gentiobiose (&beta;-D-glucopyranosyl-1,6-D-glucose) in addition to glucose during degradation of &beta;-1,3/1,6-glucan<CITE>REF2</CITE><CITE>REF3</CITE>.
+
The majority of the members in this family are [[exo]]-glucan-1,3-&beta;-glucosidases (EC [{{EClink}}3.2.1.58 3.2.1.58]), which cleave the terminal &beta;-1,3-glycosidic linkage at the non-reducing end of &beta;-1,3-glucans or &beta;-1,3/1,6-glucans (&beta;-1,3-glucan having single &beta;-1,6-glucoside side chains, also known as laminarin, from brown algae). Many produce gentiobiose (&beta;-D-glucopyranosyl-1,6-D-glucose) in addition to glucose during the degradation of &beta;-1,3/1,6-glucan <CITE>Pitson1995 Bara2003</CITE>.  Due to activity on laminarin, GH55 members may be referred to as "laminarinases." However, the physiological substrate for these enzymes might be fungal cell walls, whose major component is also &beta;-1,3/1,6-glucan.
  
Bgn13.1 from [http://en.wikipedia.org/wiki/Trichoderma_harzianum ''Trichoderma harzianum''] <CITE>REF4</CITE> and LamAI from[http://en.wikipedia.org/wiki/Trichoderma_viride ''Trichoderma viride''] <CITE>REF5</CITE> were described as endo-type enzymes (EC[http://us.expasy.org/cgi-bin/nicezyme.pl?3.2.1.39 3.2.1.39]) based on the experimental results.  
+
Bgn13.1 from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=5544 ''Hypocrea lixii''] (formerly known as ''Trichoderma harzianum'') <CITE>delaCruz1995</CITE> and LamAI from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=5547 ''Trichoderma viride''] <CITE>Nobe2003</CITE> were characterised as [[endo]]-acting enzymes (EC [{{EClink}}3.2.1.39 3.2.1.39]).
  
 
== Kinetics and Mechanism ==
 
== Kinetics and Mechanism ==
 +
Family 55 enzymes are [[inverting]] enzymes, as shown by <sup>1</sup>NMR analysis on ExgS from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=5063 ''Aspergillus phoenicis''] (formerly known as ''Aspergillus saitoi'') <CITE>Kasahara1992</CITE>. Release of &alpha;-glucose was subsequently confirmed by polarimetric analysis on family 55 enzymes from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=5051 ''Acremonium persicinum''] <CITE>Pitson1995</CITE>.  These results are consistent with many classical reports on gentiobiose-producing exo-&beta;-1,3-glucanases from fungi <CITE>Nelson1970 Nagasaki1977</CITE>, although the genes for these enzymes have not yet been described.
  
Family 55 enzymes are inverting enzyme, as shown by NMR analysis on ExgS from ''Aspergillus saitoi'' <CITE>REF6</CITE>. This result is consistent with many classical reports on gentiobiose-producing exo-&beta;-1,3-glucanases from fungi<CITE>REF7</CITE><CITE>REF8</CITE>, but the genes for these enzymes have not cloned yet.
+
== Catalytic Residues ==
 +
A crystal structure of [[exo]]-&beta;-1,3-glucanase Lam55A from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=5306 ''Phanerochaete chrysospoirum''] K-3 (PcLam55A) complexed with gluconolactone (PDB ID [{{PDBlink}}3eqo 3eqo]) suggested that Glu633 is the [[general acid]]. A candidate nucleophilic water was found near the C-1 atom of gluconolactone. A crystal structure of the bacterial enzyme SacteLam55A complexed with laminarihexaose (PDB ID [{{PDBlink}}4pf0 4pf0]), together with kinetic analysis of site-directed mutants, revealed that corresponding glutamic acid (Glu502 in SacteLam55A) also functions as the [[general acid]] in bacterial enzymes.  
  
== Catalytic Residues ==
+
The identification of the [[general base]] in this family is less clear, as is common with several other inverting GH families. In the crystal structures of both PcLam55A and SacteLam55A, the candidate nucleophilic water has no direct interaction with a sidechain carboxylate, but rather with a highly conserved glutamine residue that is, in turn, hydrogen-bonded to a conserved glutamic acid (Glu480 in SacteLam55A). Mutations of this glutamic acid (E480Q and E480A of SacteLam55A) significantly reduce catalytic activity.  Based on these kinetic and structural observations, a proton relay system for the activation of water has been proposed <CITE>Bianchetti2015</CITE>.
From the crystal structure of Lam55A from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=5306 ''Phanerochaete chrysospoirum''] complexed with gluconolactone, Glu633 appears to be the general acid. A possible nucleophilic water was found near the C-1 atom of gluconolactone, but no acidic residue that can be the general base was found around the water.
 
  
In the classical studies for exo-&beta;-1,3-glucanase from ''Basidiomycete'' QM-806, Jeffcoat and Kirkwood reported the chemical modification of histidine in the catalytic site of the enzyme caused irreversible loss of the activity, suggesting crucial role of the histidine residues <CITE>REF9</CITE>.
+
In classical studies of a [[exo]]-&beta;-1,3-glucanase from ''Sporotrichum dimorphosporum'' (formerly known as ''Basidiomycete'' QM-806), Jeffcoat and Kirkwood reported that chemical modification of histidine residues in the catalytic site of the enzyme caused irreversible loss of activity, suggesting a crucial role for this residue <CITE>Jeffcoat1987</CITE>.
  
 
== Three-dimensional structures ==
 
== Three-dimensional structures ==
The first solved 3-D structure was exo-&beta;-1,3-glucanase Lam55A from ''P. chrysosporium'' <cite>REF1</cite>. Two tandem &beta;-helix domains are positioned side by side to form a rib cage-like structure. The active site is located between the two &beta;-helix domains.
+
The first solved 3-D structure was Lam55A from ''P. chrysosporium'' <cite>Ishida2009</cite>. In this structure, two tandem &beta;-helix domains are positioned side-by-side to form a rib cage-like structure. The active site is located between the two &beta;-helix domains. A duplicated motif had been found in the primary sequence of EXG1 from ''Cochliobolus carbonum'' <cite>Nikolskaya1998</cite>, predicting the presence of two structurally similar domains in this family.
 +
 
 +
The SacteLam55A E502A structure complexed with laminarioligosaccharides revealed the positioning of the substrate in the active site and the conformation of the proposed catalytic residues. The structure also shows a solvent-exposed [[Surface Binding Site]] <CITE>Bianchetti2015</CITE>.
  
 
== Family Firsts ==
 
== Family Firsts ==
;First sterochemistry determination: Probably ExgS from ''A. saitoi'' by <sup>1</sup>H-NMR analysis <CITE>REF6</CITE>. See [[#Kinetics and Mechanism|kinetics and mechanism]].
+
;First sterochemistry determination: Probably ExgS from ''A. saitoi'' by H-NMR analysis <CITE>Kasahara1992</CITE>. See [[#Kinetics and Mechanism|kinetics and mechanism]].
 
+
;First gene cloning: BGN13.1 from ''T. harzianum'' ([http://www.uniprot.org/uniprot/P53626 Uniprot P53626]) <cite>delaCruz1995</cite> and EXG1 from [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=5017 ''C. carbonum''] (partial gene coning and gene knockout) ([http://www.uniprot.org/uniprot/P49426 Uniprot P49426]) <cite>Schaeffer1994</cite>. First bacterial gene was cloned from ''Arthrobacter'' sp. NHB-10 ([http://www.uniprot.org/uniprot/A4PHQ5 Uniprot A4PHQ5]) <cite>Okazaki2007</cite>.
;First gene cloning: BGN13.1 from ''T. harzianum''. <cite>REF7</cite>.
+
;First [[general acid]] residue identification: SacteLam55A from ''Streptmyces'' sp. SirexAA-E ([http://www.uniprot.org/uniprot/G2NFJ9 Uniprot G2NFJ9]) by crystal structure and kinetic analysis on mutants <cite>Bianchetti2015</cite>.
 
+
;First [[general base]] residue identification: SacteLam55A from ''Streptmyces'' sp. SirexAA-E ([http://www.uniprot.org/uniprot/G2NFJ9 Uniprot G2NFJ9]) by crystal structure and kinetic analysis on mutants <cite>Bianchetti2015</cite>.
;First general acid residue identification:
+
;First 3-D structure: Lam55A from ''P. chrysosporium'' by X-ray crystallography <cite>Ishida2009</cite>.
 
 
;First general base residue identification:
 
 
 
;First 3-D structure: Lam55A from ''Phanerochaete chrysosporium'' K-3 by X-ray crystallography ([http://www.rcsb.org/pdb/explore/explore.do?structureId=3EQO PDB 3eqo]) <cite>REF1</cite>.
 
  
 
== References ==
 
== References ==
 
<biblio>
 
<biblio>
#REF1 pmid=19193645
+
#Schaeffer1994 pmid=8135518
#REF2 pmid=8948426
+
#Ishida2009 pmid=19193645
#REF3 pmid=12594027
+
#Pitson1995 pmid=8948426
#REF4 pmid=7592488
+
#Bara2003 pmid=12594027
#REF5 pmid=12843664
+
#delaCruz1995 pmid=7592488
#REF6 Kasahara S, Nakajima T, Miyamoto C, Wada K, Furuichi Y, and Ichishima E. Characterization and mode of action of exo-1,3-&beta;-D-glucanase from ''Aspergillus saitoi''. J Ferment Bioeng 74 (4), 238-240 (1992).[http://dx.doi.org/10.1016/0922-338X(92)90118-E  DOI:10.1016/0922-338X(92)90118-E]
+
#Nobe2003 pmid=12843664
#REF7 pmid=5416668
+
#Kasahara1992 Kasahara S, Nakajima T, Miyamoto C, Wada K, Furuichi Y, and Ichishima E. Characterization and mode of action of exo-1,3-&beta;-D-glucanase from ''Aspergillus saitoi''. J Ferment Bioeng 74 (4), 238-240 (1992).[http://dx.doi.org/10.1016/0922-338X(92)90118-E  DOI:10.1016/0922-338X(92)90118-E]
#REF8 Nagasaki N, Saito K, and Yarnamoto S. Purification and characterization of an exo-&beta;-l,3-glucanase from a fungi imperfecti. Agric Biol Cbem 41, 493-502 (1977).[http://joi.jlc.jst.go.jp/JST.Journalarchive/bbb1961/41.493 JOI:JST.Journalarchive/bbb1961/41.493]
+
#Nelson1970 pmid=5416668
#REF9 pmid=3100526
+
#Nagasaki1977 Nagasaki N, Saito K, and Yarnamoto S. Purification and characterization of an exo-&beta;-l,3-glucanase from a fungi imperfecti. Agric Biol Cbem 41, 493-502 (1977).[http://joi.jlc.jst.go.jp/JST.Journalarchive/bbb1961/41.493 JOI:JST.Journalarchive/bbb1961/41.493]
 
+
#Jeffcoat1987 pmid=3100526
 +
#Nikolskaya1998 pmid=9838227
 +
#Bianchetti2015 pmid=25752603
 +
#Okazaki2007 pmid=17587693
 
</biblio>
 
</biblio>
  
[[Category:Glycoside Hydrolase Families|GH055]]'''
+
[[Category:Glycoside Hydrolase Families|GH055]]

Latest revision as of 14:15, 18 December 2021

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Glycoside Hydrolase Family 55
Clan none
Mechanism inverting
Active site residues not known
CAZy DB link
http://www.cazy.org/GH55.html

Substrate specificities

Glycoside Hydrolase family 55 consists exclusively of β-1,3-glucanases, including both exo- and endo-enzymes. All biochemically characterized members of this family had been limited to fungal enzymes until the extensive work by Bianchetti, Takasuka, et al., who reported the crystallography of exo-β-1,3-glucanase SacteLam55A from Streptmyces sp. SirexAA-E (Uniprot G2NFJ9), together with characterization of many other bacterial enzymes [1].

The majority of the members in this family are exo-glucan-1,3-β-glucosidases (EC 3.2.1.58), which cleave the terminal β-1,3-glycosidic linkage at the non-reducing end of β-1,3-glucans or β-1,3/1,6-glucans (β-1,3-glucan having single β-1,6-glucoside side chains, also known as laminarin, from brown algae). Many produce gentiobiose (β-D-glucopyranosyl-1,6-D-glucose) in addition to glucose during the degradation of β-1,3/1,6-glucan [2, 3]. Due to activity on laminarin, GH55 members may be referred to as "laminarinases." However, the physiological substrate for these enzymes might be fungal cell walls, whose major component is also β-1,3/1,6-glucan.

Bgn13.1 from Hypocrea lixii (formerly known as Trichoderma harzianum) [4] and LamAI from Trichoderma viride [5] were characterised as endo-acting enzymes (EC 3.2.1.39).

Kinetics and Mechanism

Family 55 enzymes are inverting enzymes, as shown by 1NMR analysis on ExgS from Aspergillus phoenicis (formerly known as Aspergillus saitoi) [6]. Release of α-glucose was subsequently confirmed by polarimetric analysis on family 55 enzymes from Acremonium persicinum [2]. These results are consistent with many classical reports on gentiobiose-producing exo-β-1,3-glucanases from fungi [7, 8], although the genes for these enzymes have not yet been described.

Catalytic Residues

A crystal structure of exo-β-1,3-glucanase Lam55A from Phanerochaete chrysospoirum K-3 (PcLam55A) complexed with gluconolactone (PDB ID 3eqo) suggested that Glu633 is the general acid. A candidate nucleophilic water was found near the C-1 atom of gluconolactone. A crystal structure of the bacterial enzyme SacteLam55A complexed with laminarihexaose (PDB ID 4pf0), together with kinetic analysis of site-directed mutants, revealed that corresponding glutamic acid (Glu502 in SacteLam55A) also functions as the general acid in bacterial enzymes.

The identification of the general base in this family is less clear, as is common with several other inverting GH families. In the crystal structures of both PcLam55A and SacteLam55A, the candidate nucleophilic water has no direct interaction with a sidechain carboxylate, but rather with a highly conserved glutamine residue that is, in turn, hydrogen-bonded to a conserved glutamic acid (Glu480 in SacteLam55A). Mutations of this glutamic acid (E480Q and E480A of SacteLam55A) significantly reduce catalytic activity. Based on these kinetic and structural observations, a proton relay system for the activation of water has been proposed [1].

In classical studies of a exo-β-1,3-glucanase from Sporotrichum dimorphosporum (formerly known as Basidiomycete QM-806), Jeffcoat and Kirkwood reported that chemical modification of histidine residues in the catalytic site of the enzyme caused irreversible loss of activity, suggesting a crucial role for this residue [9].

Three-dimensional structures

The first solved 3-D structure was Lam55A from P. chrysosporium [10]. In this structure, two tandem β-helix domains are positioned side-by-side to form a rib cage-like structure. The active site is located between the two β-helix domains. A duplicated motif had been found in the primary sequence of EXG1 from Cochliobolus carbonum [11], predicting the presence of two structurally similar domains in this family.

The SacteLam55A E502A structure complexed with laminarioligosaccharides revealed the positioning of the substrate in the active site and the conformation of the proposed catalytic residues. The structure also shows a solvent-exposed Surface Binding Site [1].

Family Firsts

First sterochemistry determination
Probably ExgS from A. saitoi by H-NMR analysis [6]. See kinetics and mechanism.
First gene cloning
BGN13.1 from T. harzianum (Uniprot P53626) [4] and EXG1 from C. carbonum (partial gene coning and gene knockout) (Uniprot P49426) [12]. First bacterial gene was cloned from Arthrobacter sp. NHB-10 (Uniprot A4PHQ5) [13].
First general acid residue identification
SacteLam55A from Streptmyces sp. SirexAA-E (Uniprot G2NFJ9) by crystal structure and kinetic analysis on mutants [1].
First general base residue identification
SacteLam55A from Streptmyces sp. SirexAA-E (Uniprot G2NFJ9) by crystal structure and kinetic analysis on mutants [1].
First 3-D structure
Lam55A from P. chrysosporium by X-ray crystallography [10].

References

  1. Bianchetti CM, Takasuka TE, Deutsch S, Udell HS, Yik EJ, Bergeman LF, and Fox BG. (2015). Active site and laminarin binding in glycoside hydrolase family 55. J Biol Chem. 2015;290(19):11819-32. DOI:10.1074/jbc.M114.623579 | PubMed ID:25752603 [Bianchetti2015]
  2. Pitson SM, Seviour RJ, McDougall BM, Woodward JR, and Stone BA. (1995). Purification and characterization of three extracellular (1-->3)-beta-D-glucan glucohydrolases from the filamentous fungus Acremonium persicinum. Biochem J. 1995;308 ( Pt 3)(Pt 3):733-41. DOI:10.1042/bj3080733 | PubMed ID:8948426 [Pitson1995]
  3. Bara MT, Lima AL, and Ulhoa CJ. (2003). Purification and characterization of an exo-beta-1,3-glucanase produced by Trichoderma asperellum. FEMS Microbiol Lett. 2003;219(1):81-5. DOI:10.1016/S0378-1097(02)01191-6 | PubMed ID:12594027 [Bara2003]
  4. de la Cruz J, Pintor-Toro JA, Benítez T, Llobell A, and Romero LC. (1995). A novel endo-beta-1,3-glucanase, BGN13.1, involved in the mycoparasitism of Trichoderma harzianum. J Bacteriol. 1995;177(23):6937-45. DOI:10.1128/jb.177.23.6937-6945.1995 | PubMed ID:7592488 [delaCruz1995]
  5. Nobe R, Sakakibara Y, Fukuda N, Yoshida N, Ogawa K, and Suiko M. (2003). Purification and characterization of laminaran hydrolases from Trichoderma viride. Biosci Biotechnol Biochem. 2003;67(6):1349-57. DOI:10.1271/bbb.67.1349 | PubMed ID:12843664 [Nobe2003]
  6. Kasahara S, Nakajima T, Miyamoto C, Wada K, Furuichi Y, and Ichishima E. Characterization and mode of action of exo-1,3-β-D-glucanase from Aspergillus saitoi. J Ferment Bioeng 74 (4), 238-240 (1992).DOI:10.1016/0922-338X(92)90118-E

    [Kasahara1992]
  7. Nelson TE (1970). The hydrolytic mechanism of an exo-beta-(1--3)-D-glucanase. J Biol Chem. 1970;245(4):869-72. | Google Books | Open Library PubMed ID:5416668 [Nelson1970]
  8. Nagasaki N, Saito K, and Yarnamoto S. Purification and characterization of an exo-β-l,3-glucanase from a fungi imperfecti. Agric Biol Cbem 41, 493-502 (1977).JOI:JST.Journalarchive/bbb1961/41.493

    [Nagasaki1977]
  9. Jeffcoat R and Kirkwood S. (1987). Implication of histidine at the active site of exo-beta-(1-3)-D-glucanase from Basidiomycete sp. QM 806. J Biol Chem. 1987;262(3):1088-91. | Google Books | Open Library PubMed ID:3100526 [Jeffcoat1987]
  10. Ishida T, Fushinobu S, Kawai R, Kitaoka M, Igarashi K, and Samejima M. (2009). Crystal structure of glycoside hydrolase family 55 {beta}-1,3-glucanase from the basidiomycete Phanerochaete chrysosporium. J Biol Chem. 2009;284(15):10100-9. DOI:10.1074/jbc.M808122200 | PubMed ID:19193645 [Ishida2009]
  11. Nikolskaya AN, Pitkin JW, Schaeffer HJ, Ahn JH, and Walton JD. (1998). EXG1p, a novel exo-beta1,3-glucanase from the fungus Cochliobolus carbonum, contains a repeated motif present in other proteins that interact with polysaccharides. Biochim Biophys Acta. 1998;1425(3):632-6. DOI:10.1016/s0304-4165(98)00117-2 | PubMed ID:9838227 [Nikolskaya1998]
  12. Schaeffer HJ, Leykam J, and Walton JD. (1994). Cloning and targeted gene disruption of EXG1, encoding exo-beta 1, 3-glucanase, in the phytopathogenic fungus Cochliobolus carbonum. Appl Environ Microbiol. 1994;60(2):594-8. DOI:10.1128/aem.60.2.594-598.1994 | PubMed ID:8135518 [Schaeffer1994]
  13. Okazaki K, Nishimura N, Matsuoka F, and Hayakawa S. (2007). Cloning and characterization of the gene encoding endo-beta-1,3-glucanase from Arthrobacter sp. NHB-10. Biosci Biotechnol Biochem. 2007;71(6):1568-71. DOI:10.1271/bbb.70030 | PubMed ID:17587693 [Okazaki2007]

All Medline abstracts: PubMed